An ensemble of support vector machines for predicting the membrane protein type directly from the amino acid sequence

Amino Acids
Loris Nanni, Alessandra Lumini

Abstract

Given a particular membrane protein, it is very important to know which membrane type it belongs to because this kind of information can provide clues for better understanding its function. In this work, we propose a system for predicting the membrane protein type directly from the amino acid sequence. The feature extraction step is based on an encoding technique that combines the physicochemical amino acid properties with the residue couple model. The residue couple model is a method inspired by Chou's quasi-sequence-order model that extracts the features by utilizing the sequence order effect indirectly. A set of support vector machines, each trained using a different physicochemical amino acid property combined with the residue couple model, are combined by vote rule. The success rate obtained by our system on a difficult dataset, where the sequences in a given membrane type have a low sequence identity to any other proteins of the same membrane type, are quite high, indicating that the proposed method, where the features are extracted directly from the amino acid sequence, is a feasible system for predicting the membrane protein type.

References

Jan 1, 1995·Critical Reviews in Biochemistry and Molecular Biology·K C Chou, C T Zhang
Feb 28, 1997·Journal of Molecular Biology·J CedanoE Querol
Nov 14, 1998·Biochemical and Biophysical Research Communications·K C Chou, D W Elrod
Feb 13, 1999·Journal of Protein Chemistry·G P Zhou
Apr 9, 1999·Protein Engineering·K C Chou, D W Elrod
Dec 11, 1999·Nucleic Acids Research·S Kawashima, M Kanehisa
Dec 1, 2000·Biochemical and Biophysical Research Communications·K C Chou
May 17, 2001·Proteins·G P Zhou, N Assa-Munt
Jun 21, 2001·Molecular Cell Biology Research Communications : MCBRC·Y D CaiK C Chou
Aug 21, 2002·The Journal of Biological Chemistry·Kuo-Chen Chou, Yu-Dong Cai
Dec 10, 2002·Proteins·Guo-Ping Zhou, Kutbuddin Doctor
Nov 19, 2003·Biochemical and Biophysical Research Communications·Kuo-Chen Chou, Yu-Dong Cai
Dec 25, 2003·Bioinformatics·Ying Huang, Yanda Li
Jul 14, 2004·Biochemical and Biophysical Research Communications·Kuo-Chen Chou, Yu-Dong Cai
Jul 29, 2004·Current Medicinal Chemistry·Kuo-Chen Chou
Aug 18, 2004·Protein Engineering, Design & Selection : PEDS·Meng WangKuo-Chen Chou
Oct 30, 2004·Bioinformatics·Kuo-Chen Chou, Yu-Dong Cai
Sep 6, 2005·Biochemical and Biophysical Research Communications·Hui LiuKuo-Chen Chou
Sep 8, 2005·Bioinformatics·Chittibabu Guda, Shankar Subramaniam
Jan 18, 2006·BMC Bioinformatics·Youfang CaoKexuan Tang
Feb 17, 2006·Bioinformatics·Loris Nanni, Alessandra Lumini
Jun 28, 2006·Protein and Peptide Letters·Bing NiuKuo-Chen Chou
Jul 1, 2006·Biochemical and Biophysical Research Communications·Kuo-Chen Chou, Hong-Bin Shen
Aug 8, 2006·Journal of Theoretical Biology·Sukanta MondalSuryanarayanarao Ramakumar
Aug 15, 2006·Biochemical and Biophysical Research Communications·Kanaka Durga KedarisettiScott Dick
Aug 16, 2006·Journal of Theoretical Biology·Chao ChenJin-Yuan Mo
Sep 13, 2006·Nucleic Acids Research·KiYoung LeeDoheon Lee
Sep 20, 2006·Journal of Cellular Biochemistry·Kuo-Chen Chou, Hong-Bin Shen
Oct 13, 2006·Amino Acids·H-B Shen, K-C Chou
Oct 13, 2006·Protein Engineering, Design & Selection : PEDS·Qing-Bin Gao, Zheng-Zhi Wang

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Citations

Aug 19, 2011·Amino Acids·Maqsood HayatMohammed Yeasin
Nov 7, 2009·Artificial Intelligence in Medicine·Loris Nanni, Alessandra Lumini
Oct 6, 2009·Journal of Theoretical Biology·Tong WangXiao-ming Hu
Mar 24, 2016·Journal of Theoretical Biology·Shibiao WanSun-Yuan Kung
Mar 23, 2015·The Journal of Membrane Biology·Xuan XiaoWei-Zhong Lin
Feb 22, 2012·Analytical Biochemistry·Maqsood Hayat, Asifullah Khan
Sep 4, 2015·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Shibiao WanSun-Yuan Kung
Nov 21, 2016·The Journal of Membrane Biology·Ahmad Hassan ButtYaser Daanial Khan
Aug 3, 2021·Briefings in Bioinformatics·Zilong HouXiangtao Li

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